Table 1 Proteome-based pan-cancer molecular subtypes in CPTAC Confirmatory/Discovery cohort.
Subtype | n (%) | Associated TCGA mRNA-based class | Description and notable features |
|---|---|---|---|
k1 | 22 (4.1) | c1 | Over-expression of proteasome complex proteins, glycolysis proteins, and pentose phosphate pathway proteins. |
k2 | 38 (7.1) | c3,c10 | Adaptive immune system-related; associated with T-cell activation; expression of major histocompatibility complex proteins |
k3 | 54 (10.2) | c3,c10 | Innate immune system-related; over-expression of complement system proteins; involvement of eosinophils, neutrophils, mast cells, and macrophages; hypoxia signature. |
k4 | 29 (5.5) | c5 | Represents basal-like breast cancer; over-expression of YAP1 and MYC targets. |
k5 | 113 (21.2) | c6 | Epithelial signature; normoxia signature; over-expression of YAP1 and MYC targets; over-expression of oxidative phosphorylation and TCA cycle proteins. |
k6 | 61 (11.5) | c7 | Stromal-related; over-expression of matrix metallopeptidases; Wnt and Notch pathway signatures; hypoxia signature. |
k7 | 95 (17.9) | c8 | Stromal-related; over-expression of collagen VI proteins; Wnt and Notch pathway signatures. |
k8 | 43 (8.1) | – | Over-expression of Golgi apparatus-related proteins; Ras pathway signature. |
k9 | 29 (5.5) | – | Found in clear cell renal cell carcinoma cases only; over-expression of hemoglobin complex proteins. |
k10 | 48 (9.0) | – | Over-expression of endoplasmic reticulum-related proteins and steroid biosynthesis pathway proteins. |
